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		<title>Visualization - Neutral loss visualizer</title>
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<h1>Neutral loss visualizer</h1>

<h2>Description</h2>
<p>
This plot shows the neutral loss calculated from all MS<sup>2</sup>...  MS<sup>n</sup> in the selected raw data file. 
The user can define the number of most intense fragments to use in the calculation of the neutral loss. If a recurrent neutral loss occurs, a line pattern in the plot can be observed.
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<h4>Parameters</h4>
<dl>
	<dt>X axis</dt>
    	<dd>X axis type. The user can choose from "Retention time"  or "Precursor mass"</dd>
	<dt>Retention time</dt>
    	<dd>Retention time (X axis) range.</dd>
	<dt>Precursor m/z</dt>
    	<dd>Range of precursor m/z values.</dd>
	<dt>Fragments</dt>
    	<dd>Number of most intense fragments to check for neutral loss.</dd>


</dl>

<h4>Functionality</h4>
<p>
This plot is using the third part library JfreeChart for its basic functionality. 
To zoom in, drag the mouse from left to right, selecting the area to zoom. To zoom out drag the zoom from right to left.
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<p>
<img src="neutral.png">
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<p>
The user can highlight spots in a range of m/z. This range can be for neutral loss or for the parent ion mass. 
This option appears in a submenu by making right click on the plot area.
</p>
<p>
<img src="neutral_selection1.png">
<img src="neutral_selection2.png">
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